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comparison tools/regVariation/windowSplitter.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="winSplitter" name="Make windows">
2 <description></description>
3 <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
4 <inputs>
5 <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
6 <param format="interval" name="input" type="data" label="Select data"/>
7 <param name="size" size="10" type="integer" value="500" label="Window size"/>
8 <conditional name="wintype">
9 <param name="choice" type="select" label="Make sliding windows?">
10 <option value="0" selected="true">No</option>
11 <option value="1">Yes</option>
12 </param>
13 <when value="0">
14 <param name="offset" type="hidden" value="0" />
15 </when>
16 <when value="1">
17 <param name="offset" size="10" type="integer" value="10" label="Offset size"/>
18 </when>
19 </conditional>
20 </inputs>
21 <outputs>
22 <data format="interval" name="out_file1" metadata_source="input"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="input" value="4.bed"/>
27 <param name="size" value="5000"/>
28 <param name="choice" value="1"/>
29 <param name="offset" value="4000"/>
30 <output name="out_file1" file="4_windows.bed"/>
31 </test>
32 </tests>
33 <help>
34
35 .. class:: infomark
36
37 **What it does**
38
39 This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
40
41 -----
42
43 .. class:: warningmark
44
45 **Note**
46
47 The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.
48
49 -----
50
51 .. class:: infomark
52
53 **About formats**
54
55 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
56
57 The first three BED fields (required) are::
58
59 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
60 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
61 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
62
63 The additional BED fields (optional) are::
64
65 4. name - The name of the BED line.
66 5. score - A score between 0 and 1000.
67 6. strand - Defines the strand - either '+' or '-'.
68 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
69 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
70 9. reserved - This should always be set to zero.
71 10. blockCount - The number of blocks (exons) in the BED line.
72 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
73 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
74 13. expCount - The number of experiments.
75 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
76 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
77
78 -----
79
80 **Example**
81
82 - For the following dataset::
83
84 chr22 1000 4700 NM_174568 0 +
85
86 - running this tool with **Window size as 1000**, will return::
87
88 chr22 1000 2000 NM_174568 0 +
89 chr22 2000 3000 NM_174568 0 +
90 chr22 3000 4000 NM_174568 0 +
91
92 - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
93
94 chr22 1000 2000 NM_174568 0 +
95 chr22 1500 2500 NM_174568 0 +
96 chr22 2000 3000 NM_174568 0 +
97 chr22 2500 3500 NM_174568 0 +
98 chr22 3000 4000 NM_174568 0 +
99 chr22 3500 4500 NM_174568 0 +
100
101 </help>
102
103
104 </tool>